RnoINT0085181 @ rn6
Intron Retention
Gene
ENSRNOG00000005996 | Lhx6
Description
LIM homeobox 6 [Source:RGD Symbol;Acc:1306174]
Coordinates
chr3:15431928-15433252:-
Coord C1 exon
chr3:15433169-15433252
Coord A exon
chr3:15432000-15433168
Coord C2 exon
chr3:15431928-15431999
Length
1169 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATTCCCTCCCCCTCCCCCAGGTG
3' ss Score
12.32
Exon sequences
Seq C1 exon
ATGTACTGGAAGCATGAGAGCGCCGCCCCGGCGCTGCCCGAGGGCTGCCGGTTACCGGCGGAGGGCGGCCCCACCACCGACCAG
Seq A exon
GTGAGCAAGCAAGCGAGTGGGTGAGCGTCCGGGATCCCGGGGCCAGCGTGAGCCCGGATTCAACCGGGCCCGGCCGGGTGGCGGGCGGCAGCAAGGAGGAGGGGTATTGAGTGAGCTCGGGAGAGTGTGACTGCAAGTGTGTGAGCGCGCGAGCGGGCAGGCGGGGGTGGGGGGTCGCGGAAAGCGGGAACACATTATGCAAATGTTGGAGGAATTTCTCAAAAAGCGATTTAGCAAAGACATAGGCGAATCAAGAGGAGGCGAGGCCAGTATTGTCCGTCTGAATAGGCGCTGATAGCGCCAATGCGCCAGAGGTTGTGCCGGCGCAACGCTGAGGATCTCGATGAGGGGCCGGTCCCGGGCGCTCCAAGAGTCTGGAGGGTTCTCTTTCCTCCTCCAAGAGGCCTCTCTTTTCTCTTTTTGGCCTCATTTCACTCACCGATCTCGCCCTCTTTGGCTTGGGGCTTTCCTTGGACTGGCCTTCCAAAGGCGTTTGAATCGGTGTCAATATCCCCGCTTCAATTTCCCGGCGCGCGTCGAGCGGGCGGGCGGGCGGATGCTCCCAGCGCTCTGGGTTTTATTTTCTCAACCACCACCACCACCACTACTACCACCACCACCCCCATCTCCTTTTTATTTTCTTTCTTTCTCTCTTTTCTCCTTTTTGCATTTTGTACCGAGAGTAGGAGAAGGGAGGGGTAGAGGGAGAAAAAAATTCGATTTTTAATTACTACCATTAAAAAATCAAATTTGCAATTCTTTGGGCGGCCTGATGGATCTCACTGATTGACAGTTGGAATTGACACTCTGGCTACCTCTTATCTTGGGCATTCACGACAATTTCTAATTGCAGGTAGTTTGTGTGTGTGCGCGTGTTTTTTTTTCCCCCTCAGAGGCTTGGATTGCAAAGGAACTAAGCGATTACTTCAAGAGCCACGGGTTAAGTGCAGGGAGAGGGGGAGAGAGAGGGAAAAAAACCCAATCCAAATTCAAATTGCTTCATTAGAGAGACACCGCTTTTGTGGGGAAGGGCTTTAAATGCCCACTACAAAGTTAGGACTCATTGTTCAGCGCCGGTTTATATAACAGGCGAGGGGAGGCGCTGGGCTCTGACAGCTCCGAGCCAGTTCAGCAGCCGCTGTCGCTTGCATTCCCTCCCCCTCCCCCAG
Seq C2 exon
GTGATGGCCCAGCCAGGGTCCGGCTGCAAAGCGACCACCCGCTGTCTTGAAGGGACCGCTCCGCCTGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005996:ENSRNOT00000008817:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.643 A=NA C2=0.167
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]